Pipelining ChemAxon - Accelrys EUGM 2008


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As a recent change in the ChemAxon - SciTegic collaboration, ChemAxon took over the responsibility for developing the ChemAxon Pipeline Pilot component collection with continued active support from our partner. A new, improved collection package has been released since then by ChemAxon in March 2008. The presentation covers the new components, improvements of existing components and plans for future development.

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Pipelining ChemAxon - Accelrys EUGM 2008

  1. 1. Pipelining ChemAxon Szilard Dorant Solutions for Cheminformatics
  2. 2. The Component Collection: Quick facts <ul><li>Provides access to ChemAxon tools from Pipeline Pilot </li></ul><ul><li>Free of charge </li></ul><ul><li>Open source : Java sources are also included </li></ul><ul><li>Available from ChemAxon or Accelrys </li></ul><ul><li>Latest version : 1.4 </li></ul><ul><ul><li>Released in November 2008 </li></ul></ul><ul><ul><li>Requires JChem / Marvin 5.0.1 or better </li></ul></ul><ul><ul><li>Tested against Pipeline Pilot 6.1.1 </li></ul></ul>
  3. 3. What’s new in 2008* <ul><li>Direct support and development from ChemAxon </li></ul><ul><li>3 major releases – one about every 4 months </li></ul><ul><li>6 early access releases </li></ul><ul><li>12 new user components </li></ul><ul><li>Several components significantly upgraded </li></ul>*As of November 2008 November 24 1.4 October 22 1.3.1 July 11 1.3 March 5 1.2 Date Version User interest Development
  4. 4. Available functionality <ul><li>Standardizer: structure canonicalization </li></ul><ul><li>Chemical Terms expressions for filtering and calculations (including logP, logD, pKa, HBD, HBA, Isoelectric point, PSA and more) </li></ul><ul><li>Reactor : “smart” virtual reaction processing </li></ul><ul><li>Maximum Common Substructure (MCS) based clustering </li></ul><ul><li>IUPAC Name <-> Molecule conversion (both directions) </li></ul><ul><li>JChem chemical database: insertion, search and retrieval of structures; create and drop structure tables </li></ul><ul><li>Marvin applets: structure visualization and editing </li></ul><ul><li>Major microspecies (major protonation form) </li></ul><ul><li>Microspecies distribution </li></ul><ul><li>Burden eigenvalue descriptor (BCUT) </li></ul>
  5. 5. Chemical Terms Calculator <ul><li>Use arbitrary Chemical Terms expressions </li></ul><ul><li>Results stored to arbitrary properties </li></ul><ul><li>A wide range of ChemAxon functionality can be accessed as Chemical Terms functions </li></ul>New in 1.3
  6. 6. Canonicalization with Standardizer Simple to use, but now full complexity is also available: <ul><li>Simple actions (checkboxes) </li></ul><ul><li>Configuration string (simple or XML) </li></ul><ul><li>Configuration file </li></ul>Upgraded in 1.2
  7. 7. IUPAC naming components <ul><li>IUPAC Name to Molecule </li></ul><ul><li>Molecule to IUPAC Name </li></ul><ul><li>Example “roundtrip” protocol: </li></ul>New in 1.4
  8. 8. Reactor Improvements: Upgraded in 1.4 <ul><li>Synthesis code generation </li></ul><ul><li>Output reaction mapping </li></ul><ul><li>Advanced options: </li></ul><ul><ul><li>Unambiguous only </li></ul></ul><ul><ul><li>Ignore rules: </li></ul></ul><ul><ul><ul><li>Reactivity and Exclude </li></ul></ul></ul><ul><ul><ul><li>Selectivity </li></ul></ul></ul><ul><ul><ul><li>Tolerance </li></ul></ul></ul>
  9. 9. Combinatorial Reactor Example
  10. 10. Clustering with LibMCS Maximum Common Substructure (MCS) based clustering <ul><li>Size of smallest common substructure to consider </li></ul><ul><li>Three levels of heuristics: </li></ul><ul><ul><li>Exact (no heuristics) </li></ul></ul><ul><ul><li>Fast </li></ul></ul><ul><ul><li>Very Fast </li></ul></ul><ul><li>Bond type, atom type, charge can optionally be ignored </li></ul><ul><li>Disallow “breaking” rings (default) </li></ul>Options: New in 1.4
  11. 11. JChem Base Insert <ul><li>Returns cd_id (primary key) values </li></ul><ul><li>Two input modes: </li></ul><ul><ul><li>read structure source from a specified property </li></ul></ul><ul><ul><li>if property not specified uses PP input molecule </li></ul></ul><ul><li>Insert into additional data fields* </li></ul>New features: *Under development, currently limited to string database column types <ul><li>Duplicate filtering option (using Pass and Fail ports) </li></ul>Upgraded in 1.2
  12. 12. JChem Database Search <ul><li>Several search options were added </li></ul><ul><li>Easier protocol integration and better performance due to concentrated functionality </li></ul>Upgraded in 1.2
  13. 13. JChem Base demo protocol
  14. 14. Improved error reporting <ul><li>Helps to track down problems quicker </li></ul><ul><li>More information is displayed in the error dialog: Marvin or JChem version, the current structure, etc. </li></ul><ul><li>Utility component for displaying ChemAxon environment (from 1.4) </li></ul><ul><li>If the environment variable CHEMAXON_PP_LOG_DIR is set, an even more detailed error report will be appended to the file &quot;pp_error.txt&quot; in the specified directory </li></ul>New in 1.3
  15. 15. Planned components <ul><li>JChem Cartridge for Oracle </li></ul><ul><li>Integration with Instant JChem </li></ul><ul><li>Tautomer generation </li></ul><ul><li>Conformer generation </li></ul><ul><li>Conversion of various structure file formats </li></ul><ul><ul><li>Node release cycle is fast and flexible. Please advise us on priority and additional functionality for future node development. </li></ul></ul>
  16. 16. Resources <ul><li>Download: </li></ul><ul><ul><li>http://www.chemaxon.com/integration/download.html </li></ul></ul><ul><ul><li>http://accelrys.org/pipelinepilot/chemistry.html </li></ul></ul><ul><li>Technical support forum: </li></ul><ul><ul><li>http://www.chemaxon.com/forum/forum88.html </li></ul></ul><ul><li>E-mail: </li></ul><ul><ul><li>Dorant__at__chemaxon_._com </li></ul></ul>
  17. 17. Acknowledgements <ul><li>Accelrys </li></ul><ul><ul><li>Moises Hassan </li></ul></ul><ul><ul><li>Ton van Daelen </li></ul></ul><ul><ul><li>Keith Burdick </li></ul></ul><ul><li>Informatics Matters </li></ul><ul><ul><li>Tim Dudgeon </li></ul></ul><ul><li>ChemAxon </li></ul><ul><ul><li>Gy ö rgy Pirok </li></ul></ul><ul><ul><li>Mikl ós Vargyas </li></ul></ul><ul><ul><li>Zsolt Moh á csi </li></ul></ul>